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Search of the Bacterial Genome Descriptor
Vanek, Roman ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This bachelor thesis deals with the investigation of DNA sequences of bacterial genomes. The aim is to find out whether it is possible to determine on the basis of the nucleotide tuple frequencies from which bacteria specie the examined sequence originates. The investigation results were obtained by a tool whose implementation is also a part of the work. The output of this thesis are the experiments with nucleotide tuple frequencies based on statistical calculations and decision whether this approach is beneficial or not.
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Query Language for Biological Databases
Bahurek, Tomáš ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.
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Search of the Bacterial Genome Descriptor
Vanek, Roman ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This bachelor thesis deals with the investigation of DNA sequences of bacterial genomes. The aim is to find out whether it is possible to determine on the basis of the nucleotide tuple frequencies from which bacteria specie the examined sequence originates. The investigation results were obtained by a tool whose implementation is also a part of the work. The output of this thesis are the experiments with nucleotide tuple frequencies based on statistical calculations and decision whether this approach is beneficial or not.
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Query Language for Biological Databases
Bahurek, Tomáš ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.
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